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<div class="title">moltk/substitution_matrix_data.hpp</div>  </div>
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<a href="substitution__matrix__data_8hpp.html">Go to the documentation of this file.</a><div class="fragment"><pre class="fragment"><a name="l00001"></a>00001 <span class="comment">/*</span>
<a name="l00002"></a>00002 <span class="comment">    MolTK is a Python and C++ toolkit for protein sequence/structure alignment and visualization</span>
<a name="l00003"></a>00003 <span class="comment">    Copyright (C) 2011  Christopher M. Bruns</span>
<a name="l00004"></a>00004 <span class="comment"></span>
<a name="l00005"></a>00005 <span class="comment">    This program is free software; you can redistribute it and/or modify</span>
<a name="l00006"></a>00006 <span class="comment">    it under the terms of the GNU General Public License as published by</span>
<a name="l00007"></a>00007 <span class="comment">    the Free Software Foundation; either version 2 of the License, or</span>
<a name="l00008"></a>00008 <span class="comment">    (at your option) any later version.</span>
<a name="l00009"></a>00009 <span class="comment"></span>
<a name="l00010"></a>00010 <span class="comment">    This program is distributed in the hope that it will be useful,</span>
<a name="l00011"></a>00011 <span class="comment">    but WITHOUT ANY WARRANTY; without even the implied warranty of</span>
<a name="l00012"></a>00012 <span class="comment">    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the</span>
<a name="l00013"></a>00013 <span class="comment">    GNU General Public License for more details.</span>
<a name="l00014"></a>00014 <span class="comment"></span>
<a name="l00015"></a>00015 <span class="comment">    You should have received a copy of the GNU General Public License along</span>
<a name="l00016"></a>00016 <span class="comment">    with this program; if not, write to the Free Software Foundation, Inc.,</span>
<a name="l00017"></a>00017 <span class="comment">    51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.</span>
<a name="l00018"></a>00018 <span class="comment">    </span>
<a name="l00019"></a>00019 <span class="comment">    Commercial users should ask about our dual licensing model.</span>
<a name="l00020"></a>00020 <span class="comment">    For questions contact: cmbruns@rotatingpenguin.com</span>
<a name="l00021"></a>00021 <span class="comment">*/</span>
<a name="l00022"></a>00022 
<a name="l00028"></a>00028 <span class="preprocessor">#ifndef MOLTK_SUBSTITUTION_MATRIX_DATA_HPP_</span>
<a name="l00029"></a>00029 <span class="preprocessor"></span><span class="preprocessor">#define MOLTK_SUBSTITUTION_MATRIX_DATA_HPP_</span>
<a name="l00030"></a>00030 <span class="preprocessor"></span>
<a name="l00031"></a>00031 <span class="keyword">namespace </span>moltk {
<a name="l00032"></a>00032 
<a name="l00033"></a>00033 <span class="comment">// from http://www.ncbi.nlm.nih.gov/Class/FieldGuide/BLOSUM62.txt</span>
<a name="l00034"></a><a class="code" href="namespacemoltk.html#abc7168fddcf318af57bfcf27676e5b8d">00034</a> <span class="keyword">static</span> <span class="keyword">const</span> <span class="keywordtype">char</span>* <a class="code" href="namespacemoltk.html#abc7168fddcf318af57bfcf27676e5b8d">blosum62_string</a> = <span class="stringliteral">&quot;\</span>
<a name="l00035"></a>00035 <span class="stringliteral">#  Matrix made by matblas from blosum62.iij\n\</span>
<a name="l00036"></a>00036 <span class="stringliteral">#  * column uses minimum score\n\</span>
<a name="l00037"></a>00037 <span class="stringliteral">#  BLOSUM Clustered Scoring Matrix in 1/2 Bit Units\n\</span>
<a name="l00038"></a>00038 <span class="stringliteral">#  Blocks Database = /data/blocks_5.0/blocks.dat\n\</span>
<a name="l00039"></a>00039 <span class="stringliteral">#  Cluster Percentage: &gt;= 62\n\</span>
<a name="l00040"></a>00040 <span class="stringliteral">#  Entropy =   0.6979, Expected =  -0.5209\n\</span>
<a name="l00041"></a>00041 <span class="stringliteral">   A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V  B  Z  X  *\n\</span>
<a name="l00042"></a>00042 <span class="stringliteral">A  4 -1 -2 -2  0 -1 -1  0 -2 -1 -1 -1 -1 -2 -1  1  0 -3 -2  0 -2 -1  0 -4 \n\</span>
<a name="l00043"></a>00043 <span class="stringliteral">R -1  5  0 -2 -3  1  0 -2  0 -3 -2  2 -1 -3 -2 -1 -1 -3 -2 -3 -1  0 -1 -4 \n\</span>
<a name="l00044"></a>00044 <span class="stringliteral">N -2  0  6  1 -3  0  0  0  1 -3 -3  0 -2 -3 -2  1  0 -4 -2 -3  3  0 -1 -4 \n\</span>
<a name="l00045"></a>00045 <span class="stringliteral">D -2 -2  1  6 -3  0  2 -1 -1 -3 -4 -1 -3 -3 -1  0 -1 -4 -3 -3  4  1 -1 -4 \n\</span>
<a name="l00046"></a>00046 <span class="stringliteral">C  0 -3 -3 -3  9 -3 -4 -3 -3 -1 -1 -3 -1 -2 -3 -1 -1 -2 -2 -1 -3 -3 -2 -4 \n\</span>
<a name="l00047"></a>00047 <span class="stringliteral">Q -1  1  0  0 -3  5  2 -2  0 -3 -2  1  0 -3 -1  0 -1 -2 -1 -2  0  3 -1 -4 \n\</span>
<a name="l00048"></a>00048 <span class="stringliteral">E -1  0  0  2 -4  2  5 -2  0 -3 -3  1 -2 -3 -1  0 -1 -3 -2 -2  1  4 -1 -4 \n\</span>
<a name="l00049"></a>00049 <span class="stringliteral">G  0 -2  0 -1 -3 -2 -2  6 -2 -4 -4 -2 -3 -3 -2  0 -2 -2 -3 -3 -1 -2 -1 -4 \n\</span>
<a name="l00050"></a>00050 <span class="stringliteral">H -2  0  1 -1 -3  0  0 -2  8 -3 -3 -1 -2 -1 -2 -1 -2 -2  2 -3  0  0 -1 -4 \n\</span>
<a name="l00051"></a>00051 <span class="stringliteral">I -1 -3 -3 -3 -1 -3 -3 -4 -3  4  2 -3  1  0 -3 -2 -1 -3 -1  3 -3 -3 -1 -4 \n\</span>
<a name="l00052"></a>00052 <span class="stringliteral">L -1 -2 -3 -4 -1 -2 -3 -4 -3  2  4 -2  2  0 -3 -2 -1 -2 -1  1 -4 -3 -1 -4 \n\</span>
<a name="l00053"></a>00053 <span class="stringliteral">K -1  2  0 -1 -3  1  1 -2 -1 -3 -2  5 -1 -3 -1  0 -1 -3 -2 -2  0  1 -1 -4 \n\</span>
<a name="l00054"></a>00054 <span class="stringliteral">M -1 -1 -2 -3 -1  0 -2 -3 -2  1  2 -1  5  0 -2 -1 -1 -1 -1  1 -3 -1 -1 -4 \n\</span>
<a name="l00055"></a>00055 <span class="stringliteral">F -2 -3 -3 -3 -2 -3 -3 -3 -1  0  0 -3  0  6 -4 -2 -2  1  3 -1 -3 -3 -1 -4 \n\</span>
<a name="l00056"></a>00056 <span class="stringliteral">P -1 -2 -2 -1 -3 -1 -1 -2 -2 -3 -3 -1 -2 -4  7 -1 -1 -4 -3 -2 -2 -1 -2 -4 \n\</span>
<a name="l00057"></a>00057 <span class="stringliteral">S  1 -1  1  0 -1  0  0  0 -1 -2 -2  0 -1 -2 -1  4  1 -3 -2 -2  0  0  0 -4 \n\</span>
<a name="l00058"></a>00058 <span class="stringliteral">T  0 -1  0 -1 -1 -1 -1 -2 -2 -1 -1 -1 -1 -2 -1  1  5 -2 -2  0 -1 -1  0 -4 \n\</span>
<a name="l00059"></a>00059 <span class="stringliteral">W -3 -3 -4 -4 -2 -2 -3 -2 -2 -3 -2 -3 -1  1 -4 -3 -2 11  2 -3 -4 -3 -2 -4 \n\</span>
<a name="l00060"></a>00060 <span class="stringliteral">Y -2 -2 -2 -3 -2 -1 -2 -3  2 -1 -1 -2 -1  3 -3 -2 -2  2  7 -1 -3 -2 -1 -4 \n\</span>
<a name="l00061"></a>00061 <span class="stringliteral">V  0 -3 -3 -3 -1 -2 -2 -3 -3  3  1 -2  1 -1 -2 -2  0 -3 -1  4 -3 -2 -1 -4 \n\</span>
<a name="l00062"></a>00062 <span class="stringliteral">B -2 -1  3  4 -3  0  1 -1  0 -3 -4  0 -3 -3 -2  0 -1 -4 -3 -3  4  1 -1 -4 \n\</span>
<a name="l00063"></a>00063 <span class="stringliteral">Z -1  0  0  1 -3  3  4 -2  0 -3 -3  1 -1 -3 -1  0 -1 -3 -2 -2  1  4 -1 -4 \n\</span>
<a name="l00064"></a>00064 <span class="stringliteral">X  0 -1 -1 -1 -2 -1 -1 -1 -1 -1 -1 -1 -1 -1 -2  0  0 -2 -1 -1 -1 -1 -1 -4 \n\</span>
<a name="l00065"></a>00065 <span class="stringliteral">* -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4 -4  1 \n\</span>
<a name="l00066"></a>00066 <span class="stringliteral">&quot;</span>;
<a name="l00067"></a>00067 
<a name="l00068"></a><a class="code" href="namespacemoltk.html#a93f20a12ada0a094bf53d22ee6c099e0">00068</a> <span class="keyword">static</span> <span class="keyword">const</span> <span class="keywordtype">char</span>* <a class="code" href="namespacemoltk.html#a93f20a12ada0a094bf53d22ee6c099e0">pam250_string</a> = <span class="stringliteral">&quot;\</span>
<a name="l00069"></a>00069 <span class="stringliteral">#\n\</span>
<a name="l00070"></a>00070 <span class="stringliteral"># This matrix was produced by \&quot;pam\&quot; Version 1.0.6 [28-Jul-93]\n\</span>
<a name="l00071"></a>00071 <span class="stringliteral">#\n\</span>
<a name="l00072"></a>00072 <span class="stringliteral"># PAM 250 substitution matrix, scale = ln(2)/3 = 0.231049\n\</span>
<a name="l00073"></a>00073 <span class="stringliteral">#\n\</span>
<a name="l00074"></a>00074 <span class="stringliteral"># Expected score = -0.844, Entropy = 0.354 bits\n\</span>
<a name="l00075"></a>00075 <span class="stringliteral">#\n\</span>
<a name="l00076"></a>00076 <span class="stringliteral"># Lowest score = -8, Highest score = 17\n\</span>
<a name="l00077"></a>00077 <span class="stringliteral">#\n\</span>
<a name="l00078"></a>00078 <span class="stringliteral">   A  R  N  D  C  Q  E  G  H  I  L  K  M  F  P  S  T  W  Y  V  B  Z  X\n\</span>
<a name="l00079"></a>00079 <span class="stringliteral">A  2 -2  0  0 -2  0  0  1 -1 -1 -2 -1 -1 -3  1  1  1 -6 -3  0  0  0  0\n\</span>
<a name="l00080"></a>00080 <span class="stringliteral">R -2  6  0 -1 -4  1 -1 -3  2 -2 -3  3  0 -4  0  0 -1  2 -4 -2 -1  0 -1\n\</span>
<a name="l00081"></a>00081 <span class="stringliteral">N  0  0  2  2 -4  1  1  0  2 -2 -3  1 -2 -3  0  1  0 -4 -2 -2  2  1  0\n\</span>
<a name="l00082"></a>00082 <span class="stringliteral">D  0 -1  2  4 -5  2  3  1  1 -2 -4  0 -3 -6 -1  0  0 -7 -4 -2  3  3 -1\n\</span>
<a name="l00083"></a>00083 <span class="stringliteral">C -2 -4 -4 -5 12 -5 -5 -3 -3 -2 -6 -5 -5 -4 -3  0 -2 -8  0 -2 -4 -5 -3\n\</span>
<a name="l00084"></a>00084 <span class="stringliteral">Q  0  1  1  2 -5  4  2 -1  3 -2 -2  1 -1 -5  0 -1 -1 -5 -4 -2  1  3 -1\n\</span>
<a name="l00085"></a>00085 <span class="stringliteral">E  0 -1  1  3 -5  2  4  0  1 -2 -3  0 -2 -5 -1  0  0 -7 -4 -2  3  3 -1\n\</span>
<a name="l00086"></a>00086 <span class="stringliteral">G  1 -3  0  1 -3 -1  0  5 -2 -3 -4 -2 -3 -5  0  1  0 -7 -5 -1  0  0 -1\n\</span>
<a name="l00087"></a>00087 <span class="stringliteral">H -1  2  2  1 -3  3  1 -2  6 -2 -2  0 -2 -2  0 -1 -1 -3  0 -2  1  2 -1\n\</span>
<a name="l00088"></a>00088 <span class="stringliteral">I -1 -2 -2 -2 -2 -2 -2 -3 -2  5  2 -2  2  1 -2 -1  0 -5 -1  4 -2 -2 -1\n\</span>
<a name="l00089"></a>00089 <span class="stringliteral">L -2 -3 -3 -4 -6 -2 -3 -4 -2  2  6 -3  4  2 -3 -3 -2 -2 -1  2 -3 -3 -1\n\</span>
<a name="l00090"></a>00090 <span class="stringliteral">K -1  3  1  0 -5  1  0 -2  0 -2 -3  5  0 -5 -1  0  0 -3 -4 -2  1  0 -1\n\</span>
<a name="l00091"></a>00091 <span class="stringliteral">M -1  0 -2 -3 -5 -1 -2 -3 -2  2  4  0  6  0 -2 -2 -1 -4 -2  2 -2 -2 -1\n\</span>
<a name="l00092"></a>00092 <span class="stringliteral">F -3 -4 -3 -6 -4 -5 -5 -5 -2  1  2 -5  0  9 -5 -3 -3  0  7 -1 -4 -5 -2\n\</span>
<a name="l00093"></a>00093 <span class="stringliteral">P  1  0  0 -1 -3  0 -1  0  0 -2 -3 -1 -2 -5  6  1  0 -6 -5 -1 -1  0 -1\n\</span>
<a name="l00094"></a>00094 <span class="stringliteral">S  1  0  1  0  0 -1  0  1 -1 -1 -3  0 -2 -3  1  2  1 -2 -3 -1  0  0  0\n\</span>
<a name="l00095"></a>00095 <span class="stringliteral">T  1 -1  0  0 -2 -1  0  0 -1  0 -2  0 -1 -3  0  1  3 -5 -3  0  0 -1  0\n\</span>
<a name="l00096"></a>00096 <span class="stringliteral">W -6  2 -4 -7 -8 -5 -7 -7 -3 -5 -2 -3 -4  0 -6 -2 -5 17  0 -6 -5 -6 -4\n\</span>
<a name="l00097"></a>00097 <span class="stringliteral">Y -3 -4 -2 -4  0 -4 -4 -5  0 -1 -1 -4 -2  7 -5 -3 -3  0 10 -2 -3 -4 -2\n\</span>
<a name="l00098"></a>00098 <span class="stringliteral">V  0 -2 -2 -2 -2 -2 -2 -1 -2  4  2 -2  2 -1 -1 -1  0 -6 -2  4 -2 -2 -1\n\</span>
<a name="l00099"></a>00099 <span class="stringliteral">B  0 -1  2  3 -4  1  3  0  1 -2 -3  1 -2 -4 -1  0  0 -5 -3 -2  3  2 -1\n\</span>
<a name="l00100"></a>00100 <span class="stringliteral">Z  0  0  1  3 -5  3  3  0  2 -2 -3  0 -2 -5  0  0 -1 -6 -4 -2  2  3 -1\n\</span>
<a name="l00101"></a>00101 <span class="stringliteral">X  0 -1  0 -1 -3 -1 -1 -1 -1 -1 -1 -1 -1 -2 -1  0  0 -4 -2 -1 -1 -1 -1\n\</span>
<a name="l00102"></a>00102 <span class="stringliteral">&quot;</span>;
<a name="l00103"></a>00103 
<a name="l00104"></a>00104 } <span class="comment">// namespace moltk</span>
<a name="l00105"></a>00105 
<a name="l00106"></a>00106 <span class="preprocessor">#endif // MOLTK_SUBSTITUTION_MATRIX_DATA_HPP_</span>
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